التفاصيل البيبلوغرافية
| العنوان: |
Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods |
| المؤلفون: |
Martin, Guillaume, Baurens, Franc-Christophe, Droc, Gaëtan, Rouard, Mathieu, Cenci, Alberto, Kilian, Andrzej, Hastie, Alex, Doležel, Jaroslav, Aury, Jean-Marc, Alberti, Adriana, Carreel, Françoise, D’Hont, Angélique |
| بيانات النشر: |
BioMed Central Ltd. |
| سنة النشر: |
2016 |
| المجموعة: |
BioMed Central |
| مصطلحات موضوعية: |
Musa acuminata, Genome assembly, Bioinformatics tool, Paired-end sequences, GBS, Genome map |
| الوصف: |
Background Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana ( Musa acuminata ). Results We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80 %), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5 % of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70 %. Unknown sites (N) were reduced from 17.3 to 10.0 %. Conclusion The release of the Musa acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in other ... |
| نوع الوثيقة: |
article in journal/newspaper |
| اللغة: |
English |
| العلاقة: |
http://www.biomedcentral.com/1471-2164/17/243Test |
| الإتاحة: |
http://www.biomedcentral.com/1471-2164/17/243Test |
| حقوق: |
Copyright 2016 Martin et al. |
| رقم الانضمام: |
edsbas.7B396524 |
| قاعدة البيانات: |
BASE |
